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BASEML (in paml version 4.7, January 2013) Alignments/alignment.phylip F84 dGamma (ncatG=5)
Nonhomo: 4 fix_kappa 0
Frequencies..
T C A G
Homo_sapie 0.20270 0.16216 0.36937 0.26577
Pan_troglo 0.19820 0.16667 0.36937 0.26577
Gorilla_go 0.20721 0.15766 0.36937 0.26577
Pongo_pygm 0.20270 0.16216 0.36937 0.26577
Macaca_mul 0.19369 0.16667 0.37387 0.26577
Homogeneity statistic: X2 = 0.00092 G = 0.00092
Average 0.20090 0.16306 0.37027 0.26577
# constant sites: 218 (98.20%)
ln Lmax (unconstrained) = -316.049385
Distances: F84 (kappa) (alpha set at 0.50)
This matrix is not used in later m.l. analysis.
Homo_sapie
Pan_troglo -0.0000(-0.5000)
Gorilla_go -0.0000(-0.5000) -0.0000(-0.5000)
Pongo_pygm 0.0000(-0.5000) -0.0000(-0.5000) -0.0000(-0.5000)
Macaca_mul 0.0092( 0.4161) 0.0139( 1.3980) 0.0139( 1.4011) 0.0092( 0.4161)
TREE # 1: (((1, 2), 3), 4, 5); MP score: 4.00
lnL(ntime: 7 np: 39): -319.978730 +0.000000
6..7 7..8 8..1 8..2 7..3 6..4 6..5
0.000004 0.000004 0.000004 0.000148 0.000509 0.000004 0.000142 4.242679 5.446077 5.548261 68.505687 73.309455 4.336845 1.364788 0.150577 0.332167 0.289014 0.000000 0.000083 0.992183 0.000000 0.000000 0.974925 0.184940 0.284831 0.303290 0.000000 0.000543 0.995496 0.202454 0.162072 0.369897 0.243143 0.220709 0.302170 0.173714 0.292814 0.298218 14.013187
tree length = 0.00082
(((Homo_sapie, Pan_troglo), Gorilla_go), Pongo_pygm, Macaca_mul);
(((Homo_sapie: 0.00000, Pan_troglo: 0.00015): 0.00000, Gorilla_go: 0.00051): 0.00000, Pongo_pygm: 0.00000, Macaca_mul: 0.00014);
Detailed output identifying parameters
kappa under F84 (in order of branches): 4.24268 5.44608 5.54826 68.50569 73.30946 4.33685 1.36479
(frequency parameters for branches) [frequencies at nodes] (see Yang & Roberts 1995 fig 1)
Node #1 ( 0.15058 0.33217 0.28901 0.22824 )
Node #2 ( 0.00000 0.00008 0.99218 0.00773 )
Node #3 ( 0.00000 0.00000 0.97493 0.02507 )
Node #4 ( 0.18494 0.28483 0.30329 0.22694 )
Node #5 ( 0.00000 0.00054 0.99550 0.00396 )
Node #6 ( 0.20245 0.16207 0.36990 0.26558 )
Node #7 ( 0.24314 0.22071 0.30217 0.23398 )
Node #8 ( 0.17371 0.29281 0.29822 0.23525 )
Note: node 6 is root.
alpha (gamma, K=5) = 14.01319
rate: 0.65711 0.84349 0.97682 1.12392 1.39866
freq: 0.20000 0.20000 0.20000 0.20000 0.20000
check convergence..
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